RetrogeneDB ID: retro_rnor_1385

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 18:21262465..21263132(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Tsen34
• Ensembl ID: ENSRNOG00000011468
• Aliases: Tsen34, LENG5, SEN34
• Description: tRNA-splicing endonuclease subunit Sen34 [Source:RefSeq peptide;Acc:NP_001006969]

Sequence

>retro_rnor_1385
GAGCAAAGTTTTCAGGATCAGAGCTCTTTGGCAGCAGAGGCCCAGCAGACCCGGGGACAGGAACTTCTAGAGAAGATCTT
GGAAGGCCAGGCTGCTAAGAAGCAGAGGCTGGAACAGGATTCAGGGGCAGATGAAGAAGGCCAAGAAGCTGGTGGAAGTG
AAGCTACCCAAGGAAGTGAGACCAGTGATGATGATCAGGCTTCTGCAGAACAGGAAGTAGCAGATTTTTCATCCCTCCAA
CCAGGACCTTCAAATGGGGTGACTCCCTTACCAAGATCAGCCCTGCTTATCTAGCTGGCCACTGCCAGACCTCGGCCTGT
AAAACCTAAGCCTCTGGACTGGCATGTGCAGACCAAAGCCTGGCCCTGTGCTGGCCGTCCTGCTCATGAGCTTTGCTACC
GCATCTACAGAGACCTGTGGGAGAGAAGCTTCTTCCTCAGTGCAGCTGGGAAGTTTGGTGGTGACTTCCTGGTCTATCCT
GGTGATCTGCTGCGTTTCCATGCTCACTACATTGCACAATGCTGGTCTGCTGAGGACCCCATCCCACTTCAGGACCTGGT
CTCTGTAGGCTGCCTGGGAAACCAGTGTCAGAAAGACTCTGCTTCTCTGCTCCCCTCAGCCTCATGGGAAGGTGATTTAT
ACTTCCCTGCAGTGGGCCAGCCTGCAG

Alignment

ORF - retro_rnor_1385 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.79 %
• Parental protein coverage: 71.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EQSFQDQSTLAAEARETRRQELLEKIVEGQAAKKQKLEQDSGADEEGQEAGGSEATQGSETSDDGQASAE
          EQSFQDQS.LAAEA..TR.QELLEKI.EGQAAKKQ.LEQDSGADEEGQEAGGSEATQGSETSDD.QASAE
Retrocopy EQSFQDQSSLAAEAQQTRGQELLEKILEGQAAKKQRLEQDSGADEEGQEAGGSEATQGSETSDDDQASAE

Parental  QEGADSSSPQPGPSNGVTPLPRSALLIQLATARPRPVKAKPLDWRVQSKDWPHAGRPAHELRYSIYRDLW
          QE.AD.SS.QPGPSNGVTPLPRSALLI.LATARPRPVK.KPLDW.VQ.K.WP.AGRPAHEL.Y.IYRDLW
Retrocopy QEVADFSSLQPGPSNGVTPLPRSALLI*LATARPRPVKPKPLDWHVQTKAWPCAGRPAHELCYRIYRDLW

Parental  ERGFFLSAAGKFGGDFLVYPGDPLRFHAHYIAQCWSAEDPIPLQDLVSAGRLG-TSVRKTLLLCSPQPDG
          ER.FFLSAAGKFGGDFLVYPGD.LRFHAHYIAQCWSAEDPIPLQDLVS.G.LG.TSVRKTLLLCSPQP.G
Retrocopy ERSFFLSAAGKFGGDFLVYPGDLLRFHAHYIAQCWSAEDPIPLQDLVSVGCLG>TSVRKTLLLCSPQPHG

Parental  KVVYTSLQWASLQ
          KV.YTSLQWASLQ
Retrocopy KVIYTSLQWASLQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.07 RPM	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1385 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1385 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1385 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000002409	1 retrocopy	retro_mmur_1488,
Mus musculus	ENSMUSG00000035585	1 retrocopy	retro_mmus_1629,
Rattus norvegicus	ENSRNOG00000011468	1 retrocopy	retro_rnor_1385 ,